Scansite 2.0 is a computational tool designed to predict cell signaling interactions by identifying short protein sequence motifs recognized by modular signaling domains, phosphorylated by protein kinases, or mediating specific interactions with ligands. The tool uses position-specific scoring matrices (PSSMs) derived from oriented peptide library and phage display experiments to predict domain-motif interactions. Scansite 2.0 includes 62 motifs for various kinase families, SH2, SH3, PDZ, 14-3-3, and PTB domains, as well as PtdIns(3,4,5)P3-specific PH domains. The current version offers significant improvements in interface, performance, and user features, including support for restricted searches, isoelectric point and molecular weight sorting, and user-defined motifs. Scansite 2.0 can search all major protein databases with reduced run times and allows for the combination of pre-compiled and user-defined motifs for dual motif searching. The tool is available via the World Wide Web at http://scansite.mit.edu.Scansite 2.0 is a computational tool designed to predict cell signaling interactions by identifying short protein sequence motifs recognized by modular signaling domains, phosphorylated by protein kinases, or mediating specific interactions with ligands. The tool uses position-specific scoring matrices (PSSMs) derived from oriented peptide library and phage display experiments to predict domain-motif interactions. Scansite 2.0 includes 62 motifs for various kinase families, SH2, SH3, PDZ, 14-3-3, and PTB domains, as well as PtdIns(3,4,5)P3-specific PH domains. The current version offers significant improvements in interface, performance, and user features, including support for restricted searches, isoelectric point and molecular weight sorting, and user-defined motifs. Scansite 2.0 can search all major protein databases with reduced run times and allows for the combination of pre-compiled and user-defined motifs for dual motif searching. The tool is available via the World Wide Web at http://scansite.mit.edu.